Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001458.1 Corchorus olitorius cultivar O-4 contig01458, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 880

Length: 1468
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30


Found at i:937 original size:2 final size:2

Alignment explanation


    Indices: 930--959  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        920 AAGACATAAT

                                                          
        930 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        960 GATCTCAACC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:1321 original size:2 final size:2

Alignment explanation


    Indices: 1314--1378  Score: 93
    Period size: 2  Copynumber: 34.5  Consensus size: 2

       1304 AAAGACAATT

                              *                                           
       1314 TA TA TA TA TA TA AA TA TA TA T- TA TA -A TA TA TA TA TA TA -A
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                                    
       1353 TA TA TA TA TA TA -A TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1379 GGTTACCCAT


Statistics
Matches: 57,  Mismatches: 2, Indels: 8
        0.85            0.03        0.12

Matches are distributed among these distances:
   1    4  0.07
   2   53  0.93

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:1351 original size:13 final size:13

Alignment explanation


    Indices: 1314--1377  Score: 112
    Period size: 13  Copynumber: 4.9  Consensus size: 13

       1304 AAAGACAATT

                         
       1314 TATATATATATAA
          1 TATATATATATAA

                          
       1327 -ATATATATTATAA
          1 TATATATA-TATAA

                         
       1340 TATATATATATAA
          1 TATATATATATAA

                         
       1353 TATATATATATAA
          1 TATATATATATAA

                        
       1366 TATATATATATA
          1 TATATATATATA

       1378 TGGTTACCCA


Statistics
Matches: 49,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
  12    7  0.14
  13   35  0.71
  14    7  0.14

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (13 bp):   
TATATATATATAA
Done.